tbuckley/cabot-search huggingface dataset:
Errors in Affiliation, Figure 3, and Supplement 4
Authors: Patrick Johnston, Gerard Walls, Hong Yoon
Journal: JAMA Oncology (2023)

Mark A. Socinski, MD; Robert M. Jotte, MD, PhD; Federico Cappuzzo, MD; Makoto Nishio, MD, PhD; Tony S. K. Mok, MD; Martin Reck, MD, PhD; Gene G. Finley, MD; Monika D. Kaul, MD; Wei Yu, PhD; Nindhana Paranthaman, MD, MBA; Ilze Bāra, MD, MBA; Howard J. West, MD
Is Appendiceal Cancer a Lynch Syndrome–Associated Cancer?—Reply
Authors: Andreana N. Holowatyj, Mary K. Washington, Carolyn Horton
Journal: JAMA Oncology (2023)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA Oncology HomeNew OnlineCurrent IssueFor Authors Podcast Journals JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2023 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA Oncology journal
Activation of cholangiocyte mTORC1 drives alcohol-induced ductular reaction
Authors: Bryan Mackowiak, Bin Gao
Journal: Hepatology (2023)

Laboratory of Liver Diseases, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD 20892, USA Correspondence Bin Gao, Laboratory of Liver Diseases, NIAAA/NIH 5625 Fishers Lane Bethesda, MD 20892 Phone: 301-443-3998. Email: [email protected]
HSV-2 triggers upregulation of MALAT1 in CD4+ T cells and promotes HIV latency reversal
Authors: Carl A. Pierce, Lip Nam Loh, Holly R. Steach, Natalia Cheshenko, Paula Preston-Hurlburt, Fengrui Zhang, Stephanie Stransky, Leah Kravets, Simone Sidoli, William Philbrick, Michel Nassar, Smita Krishnaswamy, Kevan C. Herold, Betsy C. Herold
Journal: Journal of Clinical Investigation (2023)

Herpes simplex virus type 2 (HSV-2) coinfection is associated with increased HIV-1 viral loads and expanded tissue reservoirs, but the mechanisms are not well defined. HSV-2 recurrences result in an influx of activated CD4+ T cells to sites of viral replication and an increase in activated CD4+ T cells in peripheral blood. We hypothesized that HSV-2 induces changes in these cells that facilitate HIV-1 reactivation and replication and tested this hypothesis in human CD4+ T cells and 2D10 cells, a model of HIV-1 latency. HSV-2 promoted latency reversal in HSV-2-infected and bystander 2D10 cells. Bulk and single-cell RNA-Seq studies of activated primary human CD4+ T cells identified decreased expression of HIV-1 restriction factors and increased expression of transcripts including MALAT1 that could drive HIV replication in both the HSV-2-infected and bystander cells. Transfection of 2D10 cells with VP16, an HSV-2 protein that regulates transcription, significantly upregulated MALAT1 expression, decreased trimethylation of lysine 27 on histone H3 protein, and triggered HIV latency reversal. Knockout of MALAT1 from 2D10 cells abrogated the response to VP16 and reduced the response to HSV-2 infection. These results demonstrate that HSV-2 contributes to HIV-1 reactivation through diverse mechanisms, including upregulation of MALAT1 to release epigenetic silencing.
Early Detection of Molecular Residual Disease and Risk Stratification for Stage I to III Colorectal Cancer via Circulating Tumor DNA Methylation
Authors: Shaobo Mo, Li Ye, Dongyang Wang, Lingyu Han, Shuang Zhou, Hui Wang, Weixing Dai, Yichao Wang, Wenqin Luo, Renjie Wang, Ye Xu, Sanjun Cai, Rui Liu, Zheng Wang, Guoxiang Cai
Journal: JAMA Oncology (2023)

Detection of molecular residual disease and risk stratification as early as possible may improve the treatment of patients with cancer. Efficient pragmatic tests are therefore required.
Plasticity between type 2 innate lymphoid cell subsets and amphiregulin expression regulates epithelial repair in biliary atresia
Authors: Abigail E. Russi, Pranavkumar Shivakumar, Zhenhua Luo, Jorge A. Bezerra
Journal: Hepatology (2023)

Background and Aims: Although a dysregulated type 1 immune response is integral to the pathogenesis of biliary atresia, studies in both humans and mice have uncovered a type 2 response, primarily driven by type 2 innate lymphoid cells. In nonhepatic tissues, natural type 2 innate lymphoid cell (nILC2s) regulate epithelial proliferation and tissue repair, whereas inflammatory ILC2s (iIlC2s) drive tissue inflammation and injury. The aim of this study is to determine the mechanisms used by type 2 innate lymphoid cell (ILC2) subpopulations to regulate biliary epithelial response to an injury. Approach and Results: Using Spearman correlation analysis, nILC2 transcripts, but not those of iILC2s, are positively associated with cholangiocyte abundance in biliary atresia patients at the time of diagnosis. nILC2s are identified in the mouse liver through flow cytometry. They undergo expansion and increase amphiregulin production after IL-33 administration. This drives epithelial proliferation dependent on the IL-13/IL-4Rα/STAT6 pathway as determined by decreased nILC2s and reduced epithelial proliferation in knockout strains. The addition of IL-2 promotes inter-lineage plasticity towards a nILC2 phenotype. In experimental biliary atresia induced by rotavirus, this pathway promotes epithelial repair and tissue regeneration. The genetic loss or molecular inhibition of any part of this circuit switches nILC2s to inflammatory type 2 innate lymphoid cell-like, resulting in decreased amphiregulin production, decreased epithelial proliferation, and the full phenotype of experimental biliary atresia. Conclusions: These findings identify a key function of the IL-13/IL-4Rα/STAT6 pathway in ILC2 plasticity and an alternate circuit driven by IL-2 to promote nILC2 stability and amphiregulin expression. This pathway induces epithelial homeostasis and repair in experimental biliary atresia.
Ubiquitin Ligases Siah1a/2 Control Alveolar Macrophage Functions to Limit Carcinogen-Induced Lung Adenocarcinoma
Authors: Marzia Scortegagna, Yuanning Du, Linda M. Bradley, Kun Wang, Alfredo Molinolo, Eytan Ruppin, Rabi Murad, Ze'ev A. Ronai
Journal: Cancer Research (2023)

Cellular components of the tumor microenvironment, including myeloid cells, play important roles in the progression of lung adenocarcinoma (LUAD) and its response to therapy. Here, we characterize the function of the ubiquitin ligases Siah1a/2 in regulating the differentiation and activity of alveolar macrophages (AM) and assess the implication of Siah1a/2 control of AMs for carcinogen-induced LUAD. Macrophage-specific genetic ablation of Siah1a/2 promoted accumulation of AMs with an immature phenotype and increased expression of protumorigenic and pro-inflammatory Stat3 and β-catenin gene signatures. Administration of urethane to wild-type mice promoted enrichment of immature-like AMs and lung tumor development, which was enhanced by macrophage-specific Siah1a/2 ablation. The profibrotic gene signature seen in Siah1a/2-ablated immature-like macrophages was associated with increased tumor infiltration of CD14+ myeloid cells and poorer survival of patients with LUAD. Single-cell RNA-seq confirmed the presence of a cluster of immature-like AMs expressing a profibrotic signature in lungs of patients with LUAD, a signature enhanced in smokers. These findings identify Siah1a/2 in AMs as gatekeepers of lung cancer development.The ubiquitin ligases Siah1a/2 control proinflammatory signaling, differentiation, and profibrotic phenotypes of alveolar macrophages to suppress lung carcinogenesis.
Piperacillin-Tazobactam Compared With Cefoxitin as Antimicrobial Prophylaxis for Pancreatoduodenectomy
Authors: Michael I. D’Angelica, Ryan J. Ellis, Jason B. Liu, Brian C. Brajcich, Mithat Gönen, Vanessa M. Thompson, Mark E. Cohen, Susan K. Seo, Emily C. Zabor, Michele L. Babicky, David J. Bentrem, Stephen W. Behrman, Kimberly A. Bertens, Scott A. Celinski, Carlos H. F. Chan, Mary Dillhoff, Matthew E. B. Dixon, Carlos Fernandez-del Castillo, Sepideh Gholami, Michael G. House, Paul J. Karanicolas, Harish Lavu, Shishir K. Maithel, John C. McAuliffe, Mark J. Ott, Bradley N. Reames, Dominic E. Sanford, Umut Sarpel, Courtney L. Scaife, Pablo E. Serrano, Travis Smith, Rebecca A. Snyder, Mark S. Talamonti, Sharon M. Weber, Adam C. Yopp, Henry A. Pitt, Clifford Y. Ko
Journal: JAMA (2023)

Despite improvements in perioperative mortality, the incidence of postoperative surgical site infection (SSI) remains high after pancreatoduodenectomy. The effect of broad-spectrum antimicrobial surgical prophylaxis in reducing SSI is poorly understood.
The Association of Reported Experiences of Racial and Ethnic Discrimination in Health Care with COVID-19 Vaccination Status and Intent — United States, April 22, 2021–November 26, 2022
Authors: Laurie D. Elam-Evans, Camara Phyllis Jones, Kushagra Vashist, David Yankey, Chalanda S. Smith, Jennifer L. Kriss, Peng-Jun Lu, Michael E. St. Louis, Noel T. Brewer, James A. Singleton
Journal: MMWR Morbidity and Mortality Weekly Report (2023)

In 2021, the CDC Director declared that racism is a serious threat to public health,* reflecting a growing awareness of racism as a cause of health inequities, health disparities, and disease. Racial and ethnic disparities in COVID-19-related hospitalization and death (1,2) illustrate the need to examine root causes, including experiences of discrimination. This report describes the association between reported experiences of discrimination in U.S. health care settings and COVID-19 vaccination status and intent to be vaccinated by race and ethnicity during April 22, 2021-November 26, 2022, based on the analysis of interview data collected from 1,154,347 respondents to the National Immunization Survey-Adult COVID Module (NIS-ACM). Overall, 3.5% of adults aged ≥18 years reported having worse health care experiences compared with persons of other races and ethnicities (i.e., they experienced discrimination), with significantly higher percentages reported by persons who identified as non-Hispanic Black or African American (Black) (10.7%), non-Hispanic American Indian or Alaska Native (AI/AN) (7.2%), non-Hispanic multiple or other race (multiple or other race) (6.7%), Hispanic or Latino (Hispanic) (4.5%), non-Hispanic Native Hawaiian or other Pacific Islander (NHOPI) (3.9%), and non-Hispanic Asian (Asian) (2.8%) than by non-Hispanic White (White) persons (1.6%). Unadjusted differences in prevalence of being unvaccinated against COVID-19 among respondents reporting worse health care experiences than persons of other races and ethnicities compared with those who reported that their health care experiences were the same as those of persons of other races and ethnicities were statistically significant overall (5.3) and for NHOPI (19.2), White (10.5), multiple or other race (5.7), Black (4.6), Asian (4.3), and Hispanic (2.6) adults. Findings were similar for vaccination intent. Eliminating inequitable experiences in health care settings might help reduce some disparities in receipt of a COVID-19 vaccine.
Incidence of Underlying Abnormal Findings on Routine Magnetic Resonance Imaging for Bell Palsy
Authors: Thibault Savary, Maxime Fieux, Marion Douplat, Romain Tournegros, Sophie Daubie, Dylan Pavie, Luna Denoix, Jean-Baptiste Pialat, Stephane Tringali
Journal: JAMA Network Open (2023)

Importance There is no consensus on the benefits of routine magnetic resonance imaging (MRI) of the facial nerve in patients with suspected idiopathic peripheral facial palsy (PFP) (ie, Bell palsy [BP]). Objectives To estimate the proportion of adult patients in whom MRI led to correction of an initial clinical diagnosis of BP; to determine the proportion of patients with confirmed BP who had MRI evidence of facial nerve neuritis without secondary lesions; and to identify factors associated with secondary (nonidiopathic) PFP at initial presentation and 1 month later. Design, Setting, and Participants This retrospective multicenter cohort study analyzed the clinical and radiological data of 120 patients initially diagnosed with suspected BP from January 1, 2018, to April 30, 2022, at the emergency department of 3 tertiary referral centers in France. Interventions All patients screened for clinically suspected BP underwent an MRI of the entire facial nerve with a double-blind reading of all images. Main Outcomes and Measures The proportion of patients in whom MRI led to a correction of the initial diagnosis of BP (any condition other than BP, including potentially life-threating conditions) and results of contrast enhancement of the facial nerve were described. Results Among the 120 patients initially diagnosed with suspected BP, 64 (53.3%) were men, and the mean (SD) age was 51 (18) years. Magnetic resonance imaging of the facial nerve led to a correction of the diagnosis in 8 patients (6.7%); among them, potentially life-threatening conditions that required changes in treatment were identified in 3 (37.5%). The MRI confirmed the diagnosis of BP in 112 patients (93.3%), among whom 106 (94.6%) showed evidence of facial nerve neuritis on the affected side (hypersignal on gadolinium-enhanced T1-weighted images). This was the only objective sign confirming the idiopathic nature of PFP. Conclusions and Relevance These preliminary results suggest the added value of the routine use of facial nerve MRI in suspected cases of BP. Multicentered international prospective studies should be organized to confirm these results.
Prenatal Testing: Responsibility and Reality
Authors: Rosamond Rhodes, Matthew J. Drago
Journal: The American Journal of Bioethics (2023)

Click to increase image sizeClick to decrease image sizeThis article refers to:Non-Invasive Prenatal Testing for “Non-Medical” Traits: Ensuring Consistency in Ethical Decision-Making Additional informationFundingThe author(s) reported there is no funding associated with the work featured in this article.
Advances in Ovarian Cancer Care and Unmet Treatment Needs for Patients With Platinum Resistance
Authors: Debra L. Richardson, Ramez N. Eskander, David M. O’Malley
Journal: JAMA Oncology (2023)

Platinum-based chemotherapy has been the standard of care for ovarian cancer for the past 3 decades. Although most patients respond to platinum-based treatment, emergence of platinum resistance in recurrent ovarian cancer is inevitable during the disease course. Outcomes for patients with platinum-resistant ovarian cancer are poor, and options remain limited, highlighting a substantial unmet need for new treatment options.
Association Between 5α-Reductase Inhibitors and Prostate Cancer Mortality
Authors: Michael Baboudjian, Bastien Gondran-Tellier, Charles Dariane, Gaëlle Fiard, Gaëlle Fromont, Morgan Rouprêt, Guillaume Ploussard
Journal: JAMA Oncology (2023)

Recently, several large, high-quality analyses have shown opposing results regarding the association between 5α-reductase inhibitor (5-ARI) use and prostate cancer (PCa) mortality.
Qualitative Perspectives of Emergency Nurses on Electronic Health Record Behavioral Flags to Promote Workplace Safety
Authors: Emily F. Seeburger, Rachel Gonzales, Eugenia C. South, Ari B. Friedman, Anish K. Agarwal
Journal: JAMA Network Open (2023)

Emergency nurses experience high levels of workplace violence during patient interactions. Little is known about the efficacy of behavioral flags, which are notifications embedded within electronic health records (EHRs) as a tool to promote clinician safety.To explore the perspectives of emergency nurses on EHR behavioral flags, workplace safety, and patient care.In this qualitative study, semistructured interviews were conducted with emergency nurses at an academic, urban emergency department (ED) between February 8 and March 25, 2022. Interviews were audio recorded, transcribed, and analyzed using thematic analysis. Data analysis was performed from April 2 to 13, 2022.Themes and subthemes of nursing perspectives on EHR behavioral flags were identified.This study included 25 registered emergency nurses at a large academic health system, with a mean (SD) tenure of 5 (6) years in the ED. Their mean (SD) age was 33 (7) years; 19 were women (76%) and 6 were men (24%). Participants self-reported their race as Asian (3 [12%]), Black (3 [12%]), White (15 [60%]), or multiple races (2 [8%]); 3 participants (12%) self-reported their ethnicity as Hispanic or Latinx. Five themes (with subthemes) were identified: (1) benefits of flags (useful advisory; prevents violence; engenders compassion), (2) issues with flags (administrative and process issues; unhelpful; unenforceable; bias; outdated), (3) patient transparency (patient accountability; damages patient-clinician relationship), (4) system improvements (process; built environment; human resources; zero-tolerance policies), and (5) difficulties of working in the ED (harassment and abuse; unmet mental health needs of patients; COVID-19-related strain and burnout).In this qualitative study, nursing perspectives on the utility and importance of EHR behavioral flags varied. For many, flags served as an important forewarning to approach patient interactions with more caution or use safety skills. However, nurses were skeptical of the ability of flags to prevent violence from occurring and noted concern for the unintended consequences of introducing bias into patient care. These findings suggest that changes to the deployment and utilization of flags, in concert with other safety interventions, are needed to create a safer work environment and mitigate bias.
Cancer Distribution Among Asian, Native Hawaiian, and Pacific Islander Subgroups — United States, 2015–2019
Authors: Suzanne Bock, S. Jane Henley, Mary Elizabeth O’Neil, Simple D. Singh, Trevor D. Thompson, Manxia Wu
Journal: MMWR Morbidity and Mortality Weekly Report (2023)

Non-Hispanic Asian (Asian) and non-Hispanic Native Hawaiian and Pacific Islander (NHPI) persons represent growing segments of the U.S. population (1). Epidemiologic cancer studies often aggregate Asian and NHPI persons (2,3); however, because Asian and NHPI persons are culturally, geographically, and linguistically diverse (2,4), subgroup analyses might provide insights into the distribution of health outcomes. To examine the frequency and percentage of new cancer cases among 25 Asian and NHPI subgroups, CDC analyzed the most current 2015-2019 U.S. Cancer Statistics data.* The distribution of new cancer cases among Asian and NHPI subgroups differed by sex, age, cancer type, and stage at diagnosis (for screening-detected cancers). The percentage of cases diagnosed among females ranged from 47.1% to 68.2% and among persons aged <40 years, ranged from 3.1% to 20.2%. Among the 25 subgroups, the most common cancer type varied. For example, although breast cancer was the most common in 18 subgroups, lung cancer was the most common cancer among Chamoru, Micronesian race not otherwise specified (NOS), and Vietnamese persons; colorectal cancer was the most common cancer among Cambodian, Hmong, Laotian, and Papua New Guinean persons. The frequency of late-stage cancer diagnoses among all subgroups ranged from 25.7% to 40.3% (breast), 38.1% to 61.1% (cervical), 52.4% to 64.7% (colorectal), and 70.0% to 78.5% (lung). Subgroup data illustrate health disparities among Asian and NHPI persons, which might be reduced through the design and implementation of culturally and linguistically responsive cancer prevention and control programs, including programs that address social determinants of health.
Performance of 20 rapid antigen detection tests to detect SARS-CoV-2 B.1.617.2 (Delta) and B.1.1.529 (Omicron) variants using a clinical specimen panel from January 2022, Berlin, Germany
Authors: Andreas Puyskens, Fatimanur Bayram, Akin Sesver, Janine Michel, Eva Krause, Daniel Bourquain, Angela Filomena, Katharina Esser-Nobis, Carla Steffanowski, C Micha Nübling, Heinrich Scheiblauer, Lars Schaade, Andreas Nitsche
Journal: Eurosurveillance (2023)

BackgroundThere are conflicting reports on the performance of rapid antigen detection tests (RDT) in the detection of the SARS-CoV-2 Omicron (B.1.1.529) variant; however, these tests continue to be used frequently to detect potentially contagious individuals with high viral loads.AimThe aim of this study was to investigate comparative detection of the Delta (B.1.617.2) and Omicron variants by using a selection of 20 RDT and a limited panel of pooled combined oro- and nasopharyngeal clinical Delta and Omicron specimens.MethodsWe tested 20 CE-marked RDT for their performance to detect SARS-CoV-2 Delta and Omicron by using a panel of pooled clinical specimens collected in January 2022 in Berlin, Germany.ResultsWe observed equivalent detection performance for Delta and Omicron for most RDT, and sensitivity was widely in line with our previous pre-Delta/Omicron evaluation. Some variation for individual RDT was observed either for Delta vs Omicron detection, or when compared with the previous evaluation, which may be explained both by different panel sizes resulting in different data robustness and potential limitation of batch-to-batch consistency. Additional experiments with three RDT using non-pooled routine clinical samples confirmed comparable performance to detect Delta vs Omicron. Overall, RDT that were previously positively evaluated retained good performance also for Delta and Omicron variants.ConclusionOur findings suggest that currently available RDT are sufficient for the detection of SARS-CoV-2 Delta and Omicron variants.
Epigenetic memory of environmental exposures as a mediator of liver disease
Authors: Ryan A. Hlady, Keith D. Robertson
Journal: Hepatology (2023)

Epigenetic changes are a common feature of human disease, including liver disease and its progression to liver cancer. The most frequent form of liver cancer, HCC, is unusual because most of its causes, or etiologic drivers, are known and are dominated by environmental exposures, including viral infection, alcohol abuse, and overnutrition/metabolic syndrome. The epigenome is a regulatory system overlayed on the genetic material that regulates when, where, and to what extent genes are expressed in developmental, cell type, and disease-associated contexts. Deregulation of the epigenome has emerged as a major player in the pathologic effects of liver disease driving exposures, particularly during their early phases when genetic changes are uncommon. Although it is inherent in the definition of an epigenetic process to be reversible, emerging evidence indicates that epigenetic changes persist after the removal of the exposure and contribute to long-term risk of disease progression. In other systems, environmental exposures lead to beneficial adaptive changes in expression that facilitate processes such as wound healing, and these too are driven by epigenetic changes. What remains unclear, however, is what drives the transition from a beneficial epigenetic memory to a maladaptive scar, the epigenetic processes involved in forming these memories, and whether this process can be modulated for therapeutic purposes. In this review, we discuss these concepts in relation to liver disease and more broadly using examples from other tissue types and diseases, and finally consider how epigenetic therapies could be used to reprogram maladaptive epigenetic memories to delay and/or prevent hepatocarcinogenesis.